Troubleshooting resources for errors or unexpected results


Check to see if there is a known usegalaxy.* server issue.

If the server was down when you first ran your job, try a rerun once back up. A rerun can also eliminate transient server issues too short in duration to trigger a statuspage warning.

Next, start by reviewing the troubleshooting FAQ. Common reasons and solutions for tool errors are explained. Most job errors can be resolved by correcting your input data’s format/content. Others indicate a tool setting/parameter problem. This summary FAQ links to most other support FAQs.

If you cannot determine how to fix a data/input problem, search existing Q&A topics, support FAQs, and other Galaxy resources. Someone else may have had the same problem with a posted solution. Many tools will have ongoing usage discussions. The most common data/usage issues have a dedicated FAQ.

If you are unsure about how to correct a tool usage problem, review the tool help and prior Q&A.

  • Full Tool help can be found by scrolling down on the tool form.
  • Clicking on the Tool Help icon tool-help-icon in an expanded dataset will display brief tool tips.
  • Clicking on the Job Details icon job-details-icon in an expanded dataset will allow you to review stdout and stderr messages.

If that is not enough tool usage information to solve your problem, try comparing your analysis methods with those in our tutorials:

  • Galaxy Training Network Tutorials: Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon galaxyserversGTN to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

If you think you found a software bug, review the issue FAQ and linked known issues to find out if it has already been reported and to learn how to report a new problem:

If you need help after troubleshooting on your own, or would like a suspected bug vetted, please let us know by creating a new post to this site. The more details you include, the more help we can offer. For example: include the exact tool name/version (found at the top of the tool form), input data type/source, error details, screenshots.

Thanks! The Galaxy team & community


Problems with the tutorial data
Extracting WGS reads belonging to a particular organism
RNA seq analysis: deprecated tools, updated tools, learning resources
Fatal error: exit code 1 () using bowtie2
How to merge or generate FASTA file with the same chromosome
SRA file and run fastq-dump error on local Galaxy
Question about tool errors in an older Galaxy release
Change pileup to vcf format allowing for great depth (100.000 reads)???
bam filter losing metadata
analyzing unknown DNA sequence and suggesting origin
Understanding Indels with no Additional Info in VCF Output
Error with Bowtie2 tool
From FastQ to fasta - WGS Variant Analysis
Create a Galaxy workflow to identify polymorphic sites in three individuals data - BWA error
Having issue with exome sequencing - Deprecated tool (BWA for Illumina) in older workflow
Pruning big files - Filtering SNPs
Bam file to fasta file - Genome assembly
Fatal error: exit code 1 () using cuffdiff
BWA-MEM results in "An error occurred setting metadata for this dataset"
pinned globally #5

Error executing tool: formatting problem with BED dataset